The 2.8 Å crystal structure of the dynein motor domain

Abstract

Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport. Here we report the most complete structure obtained so far, to our knowledge, of the 380-kDa motor domain of Dictyostelium discoideum cytoplasmic dynein at 2.8 Å resolution; the data are reliable enough to discuss the structure and mechanism at the level of individual amino acid residues. Features that can be clearly visualized at this resolution include the coordination of ADP in each of four distinct nucleotide-binding sites in the ring-shaped AAA(+) ATPase unit, a newly identified interaction interface between the ring and mechanical linker, and junctional structures between the ring and microtubule-binding stalk, all of which should be critical for the mechanism of dynein motility. We also identify a long-range allosteric communication pathway between the primary ATPase and the microtubule-binding sites. Our work provides a framework for understanding the mechanism of dynein-based motility.

Cytoplasmic dynein regulates its attachment to microtubules via nucleotide state-switched mechanosensing at multiple AAA domains

“…AAA1 activity appears not to be strictly synchronized to that of the other AAA domains (4,10,25) and AAA3 hydrolyzes ATP an order of magnitude slower than AAA1 (34). Thus, AAA3 may be ADP bound only at "appropriate" points in the cycle, such as when the head is detached from the MT or when the rear head AAA1 binds ATP (thereby assisting in MT release).…”

“…1A). AAA1-4 bind nucleotides, whereas AAA5 and -6 are structural (3,4). A ∼15-nm "stalk" emerging from AAA4 (3,4) separates the AAA modules from the MT-binding domain (MTBD).…”

“…AAA1-4 bind nucleotides, whereas AAA5 and -6 are structural (3,4). A ∼15-nm "stalk" emerging from AAA4 (3,4) separates the AAA modules from the MT-binding domain (MTBD). The stalk configuration influences both MT affinity and ATPase activity (5) and thereby mediates bidirectional allosteric communication between the AAA ring and the MTBD (3,6).…”

“…Most models focus exclusively on AAA1 because it is the principal site of ATP hydrolysis (4,7,(21)(22)(23)(24)(25), and ATP binding to AAA1 weakens MT affinity (4, 22). However, mutations affecting ATP binding or hydrolysis at sites other than AAA1 also have marked effects on dynein-MT binding and ATPase activity (22,23,25, 26).…”

Analyses of Dynein Heavy Chain Mutations Reveal Complex Interactions Between Dynein Motor Domains and Cellular Dynein Functions

“…arranged with respect to each other, how the linker domain arches over the top of the motor ring, how the microtubulebinding domain (MTBD) stalk and its supporting strut interact at a specific interface, and how multiple regions of the AAA domains may be able to communicate nucleotide status and hydrolysis information to neighbor rings (Carter et al 2011;Kon et al 2011;Kon et al 2012;Schmidt et al 2012). These same structures provided us with the opportunity to map our mutations onto the DHC crystal structure (Kon et al 2012) and to a portion of the microtubule-binding stalk closer to the MTBD (Carter et al 2008) to gain a better understanding of the structure/function relationships within the DHC.…”